Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTACACAATCCAGAAAAGGATACTGGCTACGTAGCCTGTGCTCTGAGCAGTACTTTGGTCCGGTTCTTCAAGAAAGATGATAGCACTTGGGATCATGAAgtaagcttgaatagatcctggagttctaactctctctttcgtgtttgatcttaag

Basic information

species Selaginella moellendorffii
transcript EFJ11187
intron # 5
splice site 5'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|169035103|gb|FE444899.1|FE444899
EST:     GTACTTTGGTCCGGTTCTTCAAGAAAGATGATAGCACTTGGGATCATGAA                         GTGGTGGTGACTGTTTCGCCGCTAAAGGTGAAGAACTGGATCTTACCCGAG
genomic: GTACTTTGGTCCGGTTCTTCAAGAAAGATGATAGCACTTGGGATCATGAAgtaagcttga ... tgatcttaagGTGGTGGTGACTGTTTCGCCGCTAAAGGTGAAGAACTGGATCTTACCCGAG
EST: gi|169024425|gb|FE434363.1|FE434363
EST:     GTACTTTGGTCCGGTTCTTCAAGAAAGATGATAGCACTTGGGATCATGAA                         GTGGTGGTGACTGTTTCGCCGCTAAAGGTGAAGAACTGGATCTTACCCGAG
genomic: GTACTTTGGTCCGGTTCTTCAAGAAAGATGATAGCACTTGGGATCATGAAgtaagcttga ... tgatcttaagGTGGTGGTGACTGTTTCGCCGCTAAAGGTGAAGAACTGGATCTTACCCGAG
EST: gi|169070383|gb|FE479348.1|FE479348
EST:     GTACTTTGGTCCGGTTCTTCAAGAAAGATGATAGCACTTGGGATCATGAA                         GTGGTGGTGACTGTTTCGCCGCTAAAGGTGAAGAACTGGATCTTACCCGAG
genomic: GTACTTTGGTCCGGTTCTTCAAGAAAGATGATAGCACTTGGGATCATGAAgtaagcttga ... tgatcttaagGTGGTGGTGACTGTTTCGCCGCTAAAGGTGAAGAACTGGATCTTACCCGAG
EST: gi|169111354|gb|FE510903.1|FE510903
EST:     GTACTTTGGTCCGGTTCTTCAAGAAAGATGATAGCACTTGGGATCATGAA                         GTGGTGGTGACTGTTTCGCCGCTAAAGGTGAAGAACTGGATCTTACCCGAG
genomic: GTACTTTGGTCCGGTTCTTCAAGAAAGATGATAGCACTTGGGATCATGAAgtaagcttga ... tgatcttaagGTGGTGGTGACTGTTTCGCCGCTAAAGGTGAAGAACTGGATCTTACCCGAG
EST: gi|169103452|gb|FE507572.1|FE507572
EST:     GTACTTTGGTCCGGTTCTTCAAGAAAGATGATAGCACTTGGGATCATGAA                         GTGGTGGTGACTGTTTCGCCGCTCAAGGTGAAGAACTGGATCTTACCCGAG
genomic: GTACTTTGGTCCGGTTCTTCAAGAAAGATGATAGCACTTGGGATCATGAAgtaagcttga ... tgatcttaagGTGGTGGTGACTGTTTCGCCGCTAAAGGTGAAGAACTGGATCTTACCCGAG
EST: gi|169064647|gb|FE471378.1|FE471378
EST:     GTACTTTGGTCCGGTTCTTCAAGAAAGATGATAGCACTTGGGATCATGAA                         GTGGTGGTGACTGTTTCGCCGCTAAAGGTGAAGAACTGGATCTTACCCGAG
genomic: GTACTTTGGTCCGGTTCTTCAAGAAAGATGATAGCACTTGGGATCATGAAgtaagcttga ... tgatcttaagGTGGTGGTGACTGTTTCGCCGCTAAAGGTGAAGAACTGGATCTTACCCGAG
EST: gi|169024411|gb|FE434362.1|FE434362
EST:     CAAGAAAGATGATAGCACTTGGGATCATGAA                         GTGGTGGTGACTGTTTCGCCGCTAAAGGTGAAGAACTGGATCTTACCCGAG
genomic: CAAGAAAGATGATAGCACTTGGGATCATGAAgtaagcttga ... tgatcttaagGTGGTGGTGACTGTTTCGCCGCTAAAGGTGAAGAACTGGATCTTACCCGAG
EST: gi|169099416|gb|FE501006.1|FE501006
EST:     GTACTTTGGTCCGGTTCTTCAAGAAAGATGATAGCACTTGGGATCATGAA                         GTGGTGGTGACTGTTTCGCCGCTAAAGGTGAAGAACTGGATCTTACCCGAG
genomic: GTACTTTGGTCCGGTTCTTCAAGAAAGATGATAGCACTTGGGATCATGAAgtaagcttga ... tgatcttaagGTGGTGGTGACTGTTTCGCCGCTAAAGGTGAAGAACTGGATCTTACCCGAG
EST: gi|169024773|gb|FE433307.1|FE433307
EST:     GTACTTTGGTCCGGTTCTTCAAGAAAGATGATAGCACTTGGGATCATGAA                         GTGGTGGTGACTGTTTCGCCGCTCAAGGTGAAGAACTGGATCTTACCCGAG
genomic: GTACTTTGGTCCGGTTCTTCAAGAAAGATGATAGCACTTGGGATCATGAAgtaagcttga ... tgatcttaagGTGGTGGTGACTGTTTCGCCGCTAAAGGTGAAGAACTGGATCTTACCCGAG
EST: gi|169064646|gb|FE471377.1|FE471377
EST:     GTACTTTGGTCCGGTTCTTCAAGAAAGATGATAGCACTTGGGATCATGAA                         GTGGTGGTGACTGTTTCGCCGCTAAAGGTGAAGAACTGGATCTTACCCGAG
genomic: GTACTTTGGTCCGGTTCTTCAAGAAAGATGATAGCACTTGGGATCATGAAgtaagcttga ... tgatcttaagGTGGTGGTGACTGTTTCGCCGCTAAAGGTGAAGAACTGGATCTTACCCGAG
EST: gi|169048832|gb|FE455299.1|FE455299
EST:     TGGTCCGGTTCTTCAAGAAAGATGATAGCACTTGGCCTCATGAA                         GTGGTGGTGACTGTTTCGCCGCTAAAGGTGAAGAACTGGATCTTACCCGAG
genomic: TGGTCCGGTTCTTCAAGAAAGATGATAGCACTTGGGATCATGAAgtaagcttga ... tgatcttaagGTGGTGGTGACTGTTTCGCCGCTAAAGGTGAAGAACTGGATCTTACCCGAG
EST: gi|169038579|gb|FE446904.1|FE446904
EST:     GTACTNTGGTCCGGTTCTTCAAGAAAGATGATAGCACTTGGGATCATGAA                         GTGGTGGTGACTGTTTCGCCGCTAAAGGTGAAGAACTGGATCTTACCCGAG
genomic: GTACTTTGGTCCGGTTCTTCAAGAAAGATGATAGCACTTGGGATCATGAAgtaagcttga ... tgatcttaagGTGGTGGTGACTGTTTCGCCGCTAAAGGTGAAGAACTGGATCTTACCCGAG
EST: gi|169069403|gb|FE479486.1|FE479486
EST:     GTACTTTGGTCCGGTTCTTCAAGAAAGATGATAGCACTTGGGATCATGAA                         GTGGTGGTGACTGTTTCGCCGCTCAAGGTGAAGAACTGGATCTTACCCGAG
genomic: GTACTTTGGTCCGGTTCTTCAAGAAAGATGATAGCACTTGGGATCATGAAgtaagcttga ... tgatcttaagGTGGTGGTGACTGTTTCGCCGCTAAAGGTGAAGAACTGGATCTTACCCGAG
EST: gi|169024774|gb|FE433308.1|FE433308
EST:     GTACTTTGGTCCGGTTCTTCAAGAAAGATGATAGCACTTGGGATCATGAA                         GTGGTGGTGACTGTTTCGCCGCTCAAGGTGAAGAACTGGATCTTACCCGAG
genomic: GTACTTTGGTCCGGTTCTTCAAGAAAGATGATAGCACTTGGGATCATGAAgtaagcttga ... tgatcttaagGTGGTGGTGACTGTTTCGCCGCTAAAGGTGAAGAACTGGATCTTACCCGAG
EST: gi|169059196|gb|FE467198.1|FE467198
EST:     GTACTTTGGTCCGGTTCTTCAAGAAAGATGATAGCACTTGGGATCATGAA                         GTGGTGGTGACTGTTTCGCCGCTAAAGGTGAAGAACTGGATCTTACCCGAG
genomic: GTACTTTGGTCCGGTTCTTCAAGAAAGATGATAGCACTTGGGATCATGAAgtaagcttga ... tgatcttaagGTGGTGGTGACTGTTTCGCCGCTAAAGGTGAAGAACTGGATCTTACCCGAG
EST: gi|169038580|gb|FE446905.1|FE446905
EST:     GTACTTTGGTCCGGTTCTTCAAGAAAGATGATAGCACTTGGGATCATGAA                         GTGGTGGTGACTGTTTCGCCGCTAAAGGTGAAGAACTGGATCTTACCCGAG
genomic: GTACTTTGGTCCGGTTCTTCAAGAAAGATGATAGCACTTGGGATCATGAAgtaagcttga ... tgatcttaagGTGGTGGTGACTGTTTCGCCGCTAAAGGTGAAGAACTGGATCTTACCCGAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 34 (upstream exon), 11 (downstream exon)
Score: 17

TTTACACAATCCAGAAAAGGATACTGGCTACGTAGCCTGTGCTCTGAGCAGTACTTTGGTCCGGTTCTTCAAGAAAGATGATAGCACTTGGGATCATGAAgtaagcttga ... tgatcttaagGTGGTGGTGACTGTTTCGCCGCTAAAGGTGAAGAACTGGATCTTACCCGAGATGCCTGGCTTGATCACGGACCTTCTCATCTCCCTGGATGATCGTTTCC




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTACACAATCCAGAAAAGGATACTGGCTACGTAGCCTGTGCTCTGAGCAGTACTTTGGTCCGGTTCTTCAAGAAAGATGATAGCACTTGGGATCATGAAgtaagcttgaatagatcctggagttctaactctctctttcgtgtttgatcttaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG